## Using rownames(importance_df) as id variables
Endpoint has data from Day 2,3,10 - might be misleading since contains CFU from different data points
## Using rownames(importance_df_day) as id variables
RF all mice/days together
## Using rownames(importance_persist) as id variables
## Using rownames(importance_persist_day) as id variables
Eliminating mice euthanized early from the RF model gives similar R^2 and MSE, bu there is a slight advantage to community OTU features of Day 0 to predict Day1 CFU. As well as the R^2 value increases with increasing features, whereas when all mice are used the day 1 R^2 only decreases with increasing features. Of note, accompaied by this is an increase in the % MSE attributed to OTU15 (Akkermansia), which has seemed to stand out in all other days/analysis.Interestingly, akkermansia does not appear to have the same relationship when compared to the same day cfu and community. This could suggest akkermansia is promoting the intial colonization of c difficile. At first glance, OTU135 (Coriobacteriaceae) seems to stand out for predicting cfu of the same day as well as from day 0.
Confusion Matrix
| 0 | 1 | class.error | |
|---|---|---|---|
| 0 | 13 | 3 | 0.187500 |
| 1 | 1 | 38 | 0.025641 |
OOB error rate = 7.2727273
Mice which were euthanized early, but the model predicts the will were not (Mouse Tag - Cage): 188 LINE, 2096 OUT, 2542 OP, 389 578
##
## Call:
## roc.formula(formula = Predict_early_euth_df$Euth_Early ~ otu_euth_probs[, 2])
##
## Data: otu_euth_probs[, 2] in 16 controls (Predict_early_euth_df$Euth_Early 0) < 39 cases (Predict_early_euth_df$Euth_Early 1).
## Area under the curve: 0.9904
##
## Call:
## roc.formula(formula = cv10f_all_resp ~ cv10f_all_pred)
##
## Data: cv10f_all_pred in 1600 controls (cv10f_all_resp 1) < 3900 cases (cv10f_all_resp 2).
## Area under the curve: 0.9839
##
## Call:
## roc.formula(formula = aucrf_data$Euth_Early ~ LOO_probs)
##
## Data: LOO_probs in 16 controls (aucrf_data$Euth_Early 0) < 39 cases (aucrf_data$Euth_Early 1).
## Area under the curve: 0.992
## null device
## 1